Nick Loman
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pathogenomenick.bsky.social
Nick Loman
@pathogenomenick.bsky.social
5.8K followers 680 following 580 posts
Public health (meta)genomics & bioinformatics, Prof @unibirmingham.bsky.social, Director @imibirmingham.bsky.social & @climb.ac.uk
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Reposted by Nick Loman
davelevitan.bsky.social
Google at its peak was basically the best information retrieval system in human history and they and every competitor decided going from there to “you didn’t want answers you wanted half-assed auto-complete 80%-wrong hallucinations” in a few years was the right idea
November 25, 2025 at 1:57 AM
Reposted by Nick Loman
alexis-madrigal.bsky.social
One of the big tidal forces of the coming years is that the baseline reliability of things you see on a screen is going to decline.

I think this has not been adequately metabolized.

This is one version, but there are a bunch of them.
davey.bsky.social Davey Alba @davey.bsky.social · 14h
NEW: AI “recipe slop” is overrunning search and social. Food creators say Google’s AI Overviews and glossy fake food pics are drowning out real, tested recipes — collapsing traffic and setting home cooks up for disaster, especially this Thanksgiving.

Gift link: www.bloomberg.com/news/article...
AI Slop Recipes Are Taking Over the Internet -- And Thanksgiving Dinner
Food bloggers see traffic dip as home cooks turn to AI, inspired by impossible pictures
www.bloomberg.com
November 25, 2025 at 9:39 PM
Reposted by Nick Loman
tprstly.com
Aye
November 21, 2025 at 11:16 PM
Reposted by Nick Loman
kevinsblake.bsky.social
Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true?

Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
The Penicillin Myth
Competing theories seek to explain inconsistencies surrounding Alexander Fleming’s famed discovery.
press.asimov.com
November 24, 2025 at 5:00 PM
Reposted by Nick Loman
volts.wtf
Today on Volts: the subset of cleantech known as "electrotech" -- solar, batteries, heat pumps, etc. -- is marching toward inevitable victory, not because it's low-emissions (though it is), but because it's more efficient & cheaper. I discuss the good news with @kingsmillbond.bsky.social.
Clean electrification is inevitable
Kingsmill Bond explains why the global march of "electrotech" has moved beyond the reach of US political interference.
www.volts.wtf
November 21, 2025 at 6:25 PM
Reposted by Nick Loman
adamjkucharski.bsky.social
Turns out interest in Metaverse had about a ~9 month half life.
November 23, 2025 at 8:51 PM
Reposted by Nick Loman
matthewcobb.bsky.social
Stand by your radios at 09:00 UK time! I’ll be on R4’s Start the Week with @adamrutherford.bsky.social talking about CRICK. Also with Alison Bashford talking about science and the occult in the history of palmistry and Charlotte Houldcroft describing her work on DNA viruses.
November 24, 2025 at 7:31 AM
Reposted by Nick Loman
wvschaik.bsky.social
Not this again

'however, standard culture methods did not yield readily cultivable microbiota.'
natureportfolio.nature.com Nature Portfolio @natureportfolio.nature.com · 4d
The findings of a study in Nature Medicine introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies. go.nature.com/44bO314 #medsky #microbiome 🧪
This is figure 6, which shows intratumoral bacterial 16S signal correlates with the oral and gut microbiota of patients with brain tumor.
November 22, 2025 at 8:14 AM
Reposted by Nick Loman
baym.lol
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Reposted by Nick Loman
carlbergstrom.com
I am by no means a prominent public intellectual, but my inbox is increasingly filled with messages from people who have been convinced by sycophantic chatbots that they have discovered revolutionary theories that entirely upend our scientific understanding of the universe.
November 21, 2025 at 2:49 AM
Reposted by Nick Loman
pathoplexus.org
1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻

Read the full update: pathoplexus.org/news/2025-11...
Graph showing the change in number of directly submitted sequences to Pathoplexus since August 2024. 0 in Aug 2024 to almost 9000 today.
November 18, 2025 at 7:01 PM
Reposted by Nick Loman
chrystalok.bsky.social
Twitter and chat gpt are down. Bad day for people who suck.
November 18, 2025 at 1:11 PM
Reposted by Nick Loman
jessicamablair.bsky.social
Really excited to say that we have been awarded a BBSRC sLola! Really looking forward to kick off this project with such a fantastic team! @webberma.bsky.social @overtonlab.bsky.social @bugsinblood.bsky.social Sara Jabbari, Dong-Hyun Kim @imibirmingham.bsky.social www.ukri.org/news/powerin...
Powering team science to unlock life’s secrets
Four world-class teams awarded major BBSRC sLoLa grants to push the frontiers of discovery in microbiology, photosynthesis, gene regulation and quantum biology.
www.ukri.org
November 18, 2025 at 9:48 AM
Reposted by Nick Loman
kgandersen.bsky.social
This is an interesting case of a patient from Chad infected with a novel arenavirus species/variant/strain, presenting with meningoencephalitis.

IMO, could be classified as a highly divergent Lassa virus strain in a new country (similar to what Togo has observed).

www.nejm.org/doi/10.1056/...
A Mammarenavirus Close to Lassa Virus in a Patient with Meningoencephalitis | NEJM
A 37-year-old man in Chad presented with a fever and a headache. An extensive evaluation identified a mammarenavirus, close to Lassa virus, in samples of cerebrospinal fluid.
www.nejm.org
November 17, 2025 at 4:47 PM
Reposted by Nick Loman
acritschristoph.bsky.social
so...personally I think this is a very poor work which is really deeply confused about what metagenomics is, why we do it, and what the key biologically relevant biases actually are.

But, hey, I know there are deep divisions in the field which can't be overcome through micro-posts.

Key table:
November 16, 2025 at 5:30 PM
Reposted by Nick Loman
theonion.com
DNA Sequencing Reveals Hitler Was Type Of Fern
DNA Sequencing Reveals Hitler Was Type Of Fern
BATH, ENGLAND—Saying the discovery shed new light on the infamous German dictator’s life, University of Bath researchers revealed DNA sequencing Friday showing that Adolf Hitler was a type of fern. “A...
theonion.com
November 14, 2025 at 11:00 PM
Reposted by Nick Loman
hswapnil.medsky.social
Whoah

EBV not only causes multiple sclerosis, it also might be the root of SLE

www.science.org/doi/10.1126/...

An EBV vaccine to rid ourselves of these horrible autoimmune conditions (and many cancers)?

#lupus #medsky #RheumSky

@christosargyrop.bsky.social
Epstein-Barr virus reprograms autoreactive B cells as antigen-presenting cells in systemic lupus erythematosus
Epstein-Barr virus reprograms autoreactive B cells as antigen-presenting cells to promote pathogenic antinuclear T and B cell responses in lupus.
www.science.org
November 13, 2025 at 11:05 PM
Reposted by Nick Loman
helenbranswell.bsky.social
The outbreak in Ethiopia is #Marburg virus, the first such outbreak for this country. 9 cases so far, including some health workers. x.com/drtedros/sta...
Tedros Adhanom Ghebreyesus on X: "#Ethiopia has confirmed the outbreak that has infected at least 9 people in the south of the country is of #Marburg virus disease. I commend Ethiopia’s @FMoHealth for its rapid and transparent response to the outbreak, and the work of the Ethiopia Public Health Institute and" / X
#Ethiopia has confirmed the outbreak that has infected at least 9 people in the south of the country is of #Marburg virus disease. I commend Ethiopia’s @FMoHealth for its rapid and transparent response to the outbreak, and the work of the Ethiopia Public Health Institute and
x.com
November 14, 2025 at 4:22 PM
Reposted by Nick Loman
aroneys.bsky.social
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
Logo of Bin Chicken (Australian white ibis) on a rubbish bin, pulling out a strand of DNA
November 13, 2025 at 10:09 AM
Reposted by Nick Loman
wiringthebrain.bsky.social
New paper with @statsepi.bsky.social and @deevybee.bsky.social in which we show there's really no evidence for a link between the gut microbiome and autism www.cell.com/neuron/fullt...
Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism
Claims that the gut microbiome causally contributes to autism regularly appear in the scientific literature and popular press. Mitchell et al. critically examine influential studies underpinning these...
www.cell.com
November 13, 2025 at 4:10 PM
Reposted by Nick Loman
adrianwoolfson.bsky.social
My review of #Crick by @matthewcobb.bsky.social has been published online by @science.org. The book is lucid, beautifully crafted, and compelling. It will instantly become the definitive guide to this extraordinary individual’s life and work.
November 13, 2025 at 8:14 PM
Reposted by Nick Loman
New primer alert! Fantastic insight into how to apply machine learning and AI in microbiology. A must read. @microbiologysociety.org @delafuentelab.bsky.social www.microbiologyresearch.org/content/jour...
Microbial Primer: Artificial intelligence for microbiologists
Artificial intelligence (AI) and machine learning (ML) are reshaping microbiology, enabling rapid antibiotic discovery, resistance prediction and clinical diagnostics. For microbiologists, the goal is...
www.microbiologyresearch.org
November 13, 2025 at 6:07 PM
Reposted by Nick Loman
gcbias.bsky.social
We don't want people to think you can see evil in the genome, but we'll call our Channel 4 documentary "Hitler's DNA: Blueprint of a dictator".
November 12, 2025 at 10:35 PM
Reposted by Nick Loman
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Nick Loman
janrosenow.bsky.social
“Heat pumps are superior in efficiency to condensing boilers, even if the heat pumps are powered by electricity from a power station burning natural gas.”

Not me saying that but the late Prof Sir David MacKay.

More in my @carbonbrief.org article 👇

interactive.carbonbrief.org/factcheck/he...
November 9, 2025 at 9:05 PM